Update sapelo_programs.py #49
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Update software versions and fix an issue with the ORCA format string where `{}` is treated like it needs an argument.
| mpirun -n $NSLOTS apptainer exec /work/jttlab/containers/molpro_mpipr.sif \ | ||
| molpro.exe input.dat --output $SLURM_SUBMIT_DIR/output.dat --nouse-logfile --directory $SCRATCH_DIR | ||
| singularity run /work/jttlab/containers/molpro-2024.1.1-mpi-gapr.sif -n $NSLOTS input.dat --output $SLURM_SUBMIT_DIR/output.dat --nouse-logfile --directory $SCRATCH_DIR |
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How much has this submit script been tested? I didn't have good luck with the runscript on Sapelo previously - it only ever reliably worked locally for me. Any indications that mpi isn't communicating properly in/outside the container?
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This is a copy-paste from what I use, and I'm running a job with it now. mpirun is already called from within the container, so it doesn't need to be called outside.
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For reference, it does have trouble communicating outside of the container, but that behavior is not unique to this submit script or use case.
| cd $scratch_dir | ||
| orca {input_name} >& $SLURM_SUBMIT_DIR/{output_name} || exit 1 | ||
| /apps/eb/ORCA/6.1.0-OpenMPI-4.1.8-GCC-13.3.0-avx2/bin/orca {input_name} >& $SLURM_SUBMIT_DIR/{output_name} || exit 1 |
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Does module load not add orca to path?
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It does, but orca complains if you use threads and don't specify the full path. I don't know why they need this.
Update software versions and fix an issue with the ORCA format string where
{}is treated like it needs an argument.